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@epigen

Computational Epigenetics

Computational Epigenetics Research and Software

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  1. CellWhisperer CellWhisperer Public

    CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets

    Jupyter Notebook 53 7

  2. MrBiomics MrBiomics Public

    MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

    Python 49 1

  3. atacseq_pipeline atacseq_pipeline Public

    Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

    Python 53 2

  4. enrichment_analysis enrichment_analysis Public

    A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

    Python 36 3

  5. KPNN KPNN Public

    Knowledge-primed neural networks

    Python 36 8

  6. crop-seq crop-seq Public archive

    Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

    Python 30 13

Repositories

Showing 10 of 46 repositories
  • cellxgene Public

    Bare clone of cellxgene

    epigen/cellxgene’s past year of commit activity
    JavaScript 0 MIT 1 1 1 Updated Apr 18, 2025
  • RnBeads_web Public

    RnBeads website and online resources

    epigen/RnBeads_web’s past year of commit activity
    HTML 1 MIT 1 0 0 Updated Apr 10, 2025
  • rnaseq_pipeline Public

    RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

    epigen/rnaseq_pipeline’s past year of commit activity
    Python 7 MIT 2 2 0 Updated Apr 4, 2025
  • fetch_ngs Public

    Workflow to Fetch Public Sequencing Data and Metadata Using iSeq and MrBiomics Module.

    epigen/fetch_ngs’s past year of commit activity
    Python 10 MIT 0 1 0 Updated Apr 3, 2025
  • MrBiomics Public

    MrBiomics: Modules & Recipes augment Bioinformatics for Multi-Omics Analyses

    epigen/MrBiomics’s past year of commit activity
    Python 49 MIT 1 25 0 Updated Apr 1, 2025
  • macrophage-regulation Public

    Integrated time series analysis and high-content CRISPR screening delineates the dynamics of macrophage immune regulation

    epigen/macrophage-regulation’s past year of commit activity
    Jupyter Notebook 3 MIT 0 0 0 Updated Mar 24, 2025
  • RnBeads Public Forked from cirruswolke/RnBeads

    Git working Repo synced to the Bioconductor: http://bioconductor.org/packages/devel/bioc/html/RnBeads.html

    epigen/RnBeads’s past year of commit activity
    R 7 13 23 1 Updated Mar 13, 2025
  • atacseq_pipeline Public

    Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

    epigen/atacseq_pipeline’s past year of commit activity
    Python 53 MIT 2 4 0 Updated Mar 10, 2025
  • dea_limma Public

    A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

    epigen/dea_limma’s past year of commit activity
    R 26 MIT 2 4 0 Updated Mar 6, 2025
  • unsupervised_analysis Public

    A general purpose Snakemake workflow and MrBiomics module to perform unsupervised analyses (dimensionality reduction & cluster analysis) and visualizations of high-dimensional data.

    epigen/unsupervised_analysis’s past year of commit activity
    Python 26 MIT 4 23 0 Updated Mar 4, 2025
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